The Last Reaper
by Boreal Peat
Summary: Harbinger needs Shepard for a specific purpose. The cycle will continue, but Order will finally have an upper-hand against Chaos. Unless this cycle finally stops them. Shepard/Garrus, alternate ending REAL CHAPTER UP
1. Prologue

Disclaimer: I do not own the Mass Effect francise and nor am I at all affiliated with Bioware, EA, or even Dark Horse. Nor do I personally know anyone who are.

I want to clarify some things: Yes, this is another "alternate ending" story. No, I didn't hate the ending as much as everyone else, but I do think it was badly written, rushed, and silly. And if the fanbase is this upset, it's a problem. EA doesn't seem to understand that their customers actually are entitled; not only did they promise a more varied ending through advertisements (putting themselves in a very possible legal battle), but these customers are very invested in the series.

This spirit is something that the company should celebrate, not condemn in a PR lie of "artistic vision", and here is why:

_Star Trek: The Original Serie_s was 79 episodes long. These episodes ranged on average from 40 to 50 minutes each. This makes them about 60 hours of content. Now, imagine that, at the end of the series, the fans received the opening credits to _Star Trek: Enterprise_. They'd be kinda pissed, don't you think?

One play-through of the three games of _Mass Effect_ comes out to 90-100 hours of game play, and has a much broader modern audience than _Star Trek_ saw in the '60s. In other words, starting out, _Mass Effect_ is a bigger universe than _Star Trek_, and could even become a bigger influence on sci-fi than _Star Trek_ could ever imagine.

So, what happens when you piss off a Trekkie?

I hope the free extended footage (which, I'm sure, was already in the works and wasn't originally going to be free) makes up for their lost image and lost sales of people who sold their games back to Gamestop, allowing me and others to quickly get used copies, keeping money away from the actual publishers and producers of the game.

* * *

_Prologue_

* * *

"Commander."

"We did it," Shepard rasped. Everything ached. Even sitting down and laying her charred back on the raised stage beside the admiral—her former captain—stung like a bitch.

Anderson managed a slight nod. "Yes. We did."

Fires and falls and the clouds of Earth swirled before them.

"It's—ah-quite the view," he said. Shepard cleared away some of that blood in her throat to answer.

"Best seats in the house."

"God. Feels like years since I had just... sat down."

"I think you earned a rest. Anderson?"

"Mm? Mm."

"Stay with me. We're almost through this."

"You did good, child. You did good. I'm... proud of you."

"Thank you, sir."

A sound, something out of the deafened and dead quiet, jarred Shepard's attention to the side. She wanted to pull her hand up with the pistol she found, but her hand fumbled with fatigue and her blind grasping brought shots of pain up from her fingers. Her eyes settled on a figure, shadowy, crawling up towards them from the ground.

Shepard blinked away the residual black-out from the G-loss of consciousness she experience earlier from the beam, wondering if she was hallucinating.

It was the child.

"What the hell?" she moaned, "You... can't be here." She turned to Anderson. "Do you see—"

Anderson's face looked cold and pained, then alarmed. His eyes flew, and with a great groan of last strength and pain, his own hand found Shepard's pistol and brought it up. Shaking aside, he pulled the trigger three times.

"Anderson! What—" The ungodly screech brought Shepard's eyes to the boy. Black blood oozed from a hole in its cheek, and it screamed something out of a nightmare, his teeth bared like some ungodly, hissing demon.

"That child... was in the transport when Earth was invaded," Anderson choked out as he crawled backwards, pistol still up. Shepard scrambled to pull herself up on the raised section, away from the creature. "I saw him die... The Reapers must have found us here." No sooner had he said that was when Shepard felt cold claws close around her shoulders and tug her up. Her neck whipped around, and she saw the growling faces of cannibals, banshees, marauders, husks.

They were taking her away.

"Commander!" Her eyes returned to Anderson. The gun clicked with the spent heat sink, and the child-husk leapt into him. The admiral gave a grunt and slammed the hilt into the small skull as best as he could. "Shepard!"

"Sir!" For the first time in so long, she felt her eyes burn with tears that wanted to form. Incessant pulling of deformed hands and claws kept her from lurching forward to help him. The rancid breath of dead and dying things hissed at her and made her face cringe as she fought. "No!"

"Don't ever stop fighting, Shepard!" he cried out. He collapsed, still in tackle, behind the raised platform as the red of the room retreated her vision.

"_Anderson!_" Her scream ripped through her torn throat. The pain and pressure took her over again. It was hard to focus. She was being taken somewhere... taken out of the Citadel. But, but the fight wasn't over. _The fight wasn't over!_

She blacked out.


	2. Chapter 1: Fighting Chance

Disclaimer: Chapter 1.

I'm… actually pretty surprised, and flattered for that matter. A lot of people already seem to have their eyes on this fic, even though I'd only put up the prologue before this chapter. I'll try my best not to disappoint, and thank you for the reviews, watches, and fav's.

And for those of you who are wondering, this isn't really the same Shepard as Glass Coffin, at least in as much as Garrus's team still being alive. I think I will still be writing her leaning towards Renegade, though ('cause Renegade is fun to write).

At the end of chapters, I'm going to do a little summary of the game mechanics and what sort of extra work would be required if this ending were in the game instead. The work required would just be a guess; I'm only using knowledge I've gained from friends who are trying to break into the game industry, so I could be wrong. And I'm not going to include voice talent, as that's quick and (fairly) cheap. Feel free to correct me for any errors.

* * *

_Chapter One – Fighting Chance_

_"But an even greater evil threatened the city: the Words of Power, remnants of ancient magic long forgotten, were being sought by Maugrim's followers to bring devastation to the North." – Neverwinter Nights_

* * *

Garrus woke up with a sharp breath of pain. For him, this return to consciousness felt all too familiar. He idly rubbed one gloved hand along the scarred side of his face as he hoisted himself up from the ground.

The next few seconds took to get his bearings and remember where he was, remember his mission. _Earth._ He looked from side to side, trying to determine where the team was, where the beam to the Citadel was.

Where Shepard was.

He pulled himself up into a standing position and whipped out his assault rifle, immediately yelling into his comm. "Commander! Shepard! Can you read me?"

Nothing.

"Commander!" He scanned the area and went in the only direction that had anything resembling a path in the rubble.

Finally, something broke through the comm static. _"Vakarian, this is Victus. We'd been receiving word from the Alliance that Hammer had been devastated."_

"Sir," Garrus grunted, "I can't say we're in good shape, but I wouldn't count us out of the fight, yet." He spotted movement in the distance, so he rolled into cover and popped the spent heat-sink from before still in his rifle. "We're not getting out of here until it's done."

"_How does it look down there?"_

"Can't say for sure. The beam is missing and I can't get a hold of anyone down here. Frankly, I'm surprised _you're_ responding."

"_We're taking a beating up here, but we're now getting a whole new worry. The big Reaper has moved up to orbit and is near enough to the Crucible that we don't know what to do. We can't risk shooting it when it's so close."_

"Harbinger moved? Why?"

"_We can't tell for certain. I've been trying to contact the Alliance, but Admiral Anderson managed to get to the beam and their communication has been tied up since. We need confirmation about what it's up to from Hackett. Can you get to Shepard?"_

"I have no idea where Shepard is." He felt a stab of pain as he admitted that. "For all I know, she got to the beam, too."

"_Find somebody down there who knows! We're putting in shots as best as we can to the rest, but it could mean nothing if that Reaper does something with the Crucible!"_

That order was easier said than done. As they spoke, hostiles closed in towards him from the distance. A good distance, thought with appreciation. He switched rifles and looked at them through the scope.

Cannibals and marauders. Well, that wasn't anything he couldn't hand—

Wait, was that a _brute? _Damn, he had to face one of those fucking _flesh tanks_ alone?

_Armor-piercing rounds it is,_ he thought bitterly. His first course of action was usually to take down those marauders, but he was going to have to take down that brute before the bastard got too close. He didn't have the luxury of any sort of decoy or turning invisible and running away once it got close. He gritted his teeth and took the first shot.

After a jerk of its neck, the brute turned towards Garrus, and charged.

Garrus never popped heat sinks between setting beads so quickly in his life. His heart was racing and he was severely wishing he did try to backpedal as the thing trampled through various kinds of concrete rubble, and just as the shadow loomed over him, his left his shields go from the shots of the marauders and cannibals also advancing.

Somehow, he had just enough grit in him to aim his gun straight up at its face, even as he could feel its drool and blood drip down onto him. The brute quaked one last time through its massive body and fell.

_Oh, thank the spirits!_

The thing made excellent cover, and though he was officially out of ammo for the sniper rifle, the assault was more than capable to take out the remainder at this point. Now, as long as a banshee doesn't pop out—

_That'd be the perfect way to end my day._

None did, but with his fight done, he advanced forward from where they were coming from, just hoping he didn't come across even more. But, it wasn't like he had a choice; there was only one direction unless he felt like trying to climb the rubble with what was surely a twisted ankle and a wrenched shoulder. Hell, it was bad enough trying to roll into cover.

His destination determined brought him to some husks, distracted by a human squad. It was easy enough to take out the hostiles. When they were clear, he ran up to assess. "I'm looking for someone who has a link up to Hackett."

"Alliance communications have gone haywire ground-side since the beam faded and the big Reaper moved," the squad leader said, or more shouted through his helmet, "We've been scrambling sense."

"Damn. Anything we can do about that?"

"We think some comm towers went down, closest one is half a click or so to the northeast. We've been trying to get there, but there've been too many swarms along the way and we're out of medi-gel. No way we could take any direct action here on out. If you could head up out front, we could give some support from behind."

Garrus really wanted to sigh and complain, but he wasn't talking to Shepard. She'd _understand_ the fatigue and the fatalism. He had to find her. "Better than standing around and waiting for the world to end. Let's get going."

* * *

Kaiden found himself at one of the communication towers after more fighting than he'd care to do after being laid out by a Reaper beam. More work than _anyone_ should have to do in such a ridiculous situation, but, of course, the situation was as patently ridiculous as it could get. A fleet of Reapers, Harbinger by the Crucible, and Shepard was... who knew. He'd found Coats earlier, but he was more injured than he was and hardly in any shape to be walking around as much as he was.

With some difficulty, Kaiden repaired the tower's main power supplies and held off another wave of Reaper forces as best he could until it could return to full broadcasting capability. When it seemed like he couldn't take another hit for the lack of medi-gel and his failing shields, the static cleared away.

"This is Major Kaiden Alenko! I got the west-bound comm tower operational! Is anyone receiving?"

There was only a short pause before, _"Impressive timing, Kaiden. I just got the east-bound done."_

"Garrus!"He gave a laugh in relief. "You really weren't kidding about being hard to kill. Do you know where Shepard is?"

"_Negative. I was hoping someone in the Alliance could enlighten me. The primarch is freaking out about Harbinger and is requesting some insight about the status of the Crucible."_

"That's what I'm trying for." He tried switching signals to command. "Major Kaiden Alenko reporting! Requesting direct correspondence with Admiral Hackett."

There was a longer pause and a hiss, making his heart stop until the silence broke and allowed it to beat again. _"Hackett here. Major, what is the status down there?"_

"Some of us are up and able, but we need time to regroup." He looked up to the burning sky, bursts of incendiary clouds peppering it with even more red light. "The... whereabouts of Commander Shepard are unknown."

"_Anderson and Shepard both managed to get to the beam, but there was a scuffle and we lost contact with them both shortly after. The Citadel arms have opened and the Crucible is in position. But the beam deactivated, anyone we send in from this point would go via ship, and it's hard to get in so close with the Reaper hovering near by."_

"Then what are our orders, sir?"

"_Hammer has finished its mission. Gather the survivors and report at a secure location and report for further orders."_

"But—"

"_Hackett out."_

* * *

Keeping with the baseline of about 2000+ EMS, your squad would still survive given the already set standard. These two would then get their own separate gameplay levels, fighting alone.

Meanwhile, the rest of your team you didn't bring with will live or die depending on conditional ground assets: Alliance assets in the case of humans (Ashley, Kaiden, James), geth for Tali, turian and/or krogan (due to the treaty) for Garrus, particular conditions regarding Shadow Brokership and asari commandos with Liara (if not tying her directly with her ME2 DLC), rachni for Javik, Ex-Cerberus and/or fleet assets for EDI. If the proper conditions are not met for that character, they are considered killed (or their body destroyed, in the case of EDI).

This chapter would mostly only require level building: two areas with determined mobs, played with the two squadmates the player chose. The capability to have you able to play as those characters should already be there. And if you didn't have high enough EMS, this whole chapter would be skipped.


	3. Chapter 2: Family

Disclaimer: Chapter 1.

Thanks dannybates and servantofclio for pointing out that I posted the wrong bloody chapter! Oy vey, my brain!

These chapters are coming out SO MUCH SLOWER than I originally intended. By, like, a lot. Oh boy, I'm so sorry guys. Promise I'll try to speed up. The whole point of this is to show that a different ending is possible with little time and effort. Unfortunately, the writing time required is going to have to be waved; I am but a fanfic writer who has two other jobs, neither of which includes writing.

Hell, Bioware managed to make their Extended ending before I even got this far. Incidentally, I do feel the new content improves it and they did as best as they could with what cards they dealt themselves. Still don't like the writing and think it's silly, but it doesn't feel so _rushed_, anymore.

* * *

_Chapter Two – Family_

"_You are indeed family. No other could have lived to oppose me in person. Of course, it will not matter in the end. Ultimately, I will prevail, and a new era will be born into the Realms." – Sarevok Anchev, Baldur's Gate_

* * *

Hackett left the console and went towards the display of the battle that was taking place just outside their own bulkheads. "What's the status so far?"

The pilot didn't even look up as he worked the displays. "Three geth fighters filled in where a turian dreadnaught tried to punch through towards the Citadel. They were destroyed by the Reaper."

"And the Crucible?"

"Nothing yet, sir."

Hackett went silent, taking the moment to let the coil of tension run past him. This was a hell of an unprecedented situation, and he still wasn't sure if the reality was going to come crashing down that this is it. He was seeing something before his eyes that was before something he only knew academically.

Ships of all forms and sizes, fighters with various amounts of damage zipping or limping, Reapers kiling, Reapers conquering, Reapers falling from the sky. Fire and shockwaves and hulls bursting, cracking, falling apart. Each burst in the battlefield represented lives lost or lives saved, and the battle was both lost and won until the Crucible came on or was destroyed. Everything he knew was being unmade.

He was seeing Armageddon before his eyes, and he willed the weight of such an impossibly heavy situation didn't crush him for just a little longer. "Looks like we have a regular Schrödinger's box, here."

* * *

Shepard woke with a million nerve ends in her skin screaming at her in pain. Somehow she only grunted in turn and tried her best to twist and turn away from whatever was trying to pull her flesh off, but hands were there to keep her from struggling. Wrenching away from their grasps brought more pain, but with the pain came clarity. The dark clouds in her vision faded and allowed her eyes to focus.

The owners of the hands were many: an asari, a human, a batarian, and… something she didn't recognize off hand. They murmured low with little enunciation, and some of the speech was outright glitching. It all flowed on top of each other without hesitation and none of the words seemed to have anything to do with how they were scrabbling to continue pulling charred bits of useless armor from her.

Those damn images from the prothean beacon came flooding into the forefront of her mind, and she felt like she was falling and unable to breathe. The passage of time didn't register. She remembered an old vid she saw once of a girl dropping down a dark shaft as hands from all sides both slowed her descent. _Which way do you want to go? Up or down?_

Shepard gasped and forced herself up again.

The crowd around her had dissipated, and a few continued to mumble as they worked some sort of tubes into the container she had been laying back in.

A collector coffin.

She pulled herself out with a groan, finding that, though she was neither in her armor nor nude, whatever her body had been covered with stuck with the sides of the coffin viciously. With all her strength, she pried herself from its walls. She was surprised she didn't feel so much pain as a result. She had been heavily wounded earlier.

The two mumbling creatures working with the tubes, neither of them of any race she recognized, reared up and set wide eyes on her. An instant later, there was a pulse in the room that felt like it was coming from... _everywhere_. The immense pressure of it knocked her down onto her knees, and she heard the tell-tale droning blare of a Reaper within it.

The two aliens, however, seemed to gain strength from the pulse. Then, they spoke, in unison, with such force that the words seemed to come from outside them. The syllables she could not parse—except "SHEPARD". Their eyes gave the unsettling glow of indoctrination.

They approached, but Shepard was still able even while they might have the immediate upper hand. She used their charge to her advantage and struck low, to their abdomens, and shoved them backwards. Before they could recover, she spotted something she could work with; there appeared to be a ledge through the door behind them. She took a run forward and shoved one, succeeding in pushing them over. The other, advancing to her rear, had a similar fate when she flung it over her shoulder. She watched and examined where they fell, and finally took in her surroundings.

Low light, seams sliding organically into the walls instead of the blocky bulkheads of most ships' inner hulls, cords slung and connected from area to area like umbilical cords… she'd seen a place like this before. Formed instead of constructed. The derelict Reaper.

She was _inside_ a goddamn living Reaper.

And, in a level below her, where she had thrown over the unknown creature, there were dozens more milling about, some like what she'd just encountered, some familiar, and some she'd still have yet to have seen before then.

Suddenly, it made sense. The pulse from earlier felt much like when she'd encountered Project Rho, except she felt that energy specifically from the artifact. Here, the electricity was prickling at her from _every_ angle. These aliens—whatever they were—were no doubt indoctrinated slaves of the Reaper she was inside. Damn, hell of a setback.

At least, if nothing else, the ruined armor from before was off of her, though what she was now clothed with looked too close to Collector skin for her comfort. Similar to the armor she collected in her campaign against them so many months ago. Add to that, she felt _much_ better. The Cerberus-issued implants must have done their work in restoring her, though she was far from full functionality. At least _that_ was something the Illusive Man succeeded in.

And in that was another sliver of Good News: Though she didn't have an omni-tool or any other proper equipment, her various subdermal implants were certainly still exactly where they were, including her communicator. She fired it up, hoping it could work without amplification or a signal reroute. "This is Commander Shepard of the Normandy SR-2. Requesting radio check."

Static.

"Anyone on this frequency—this is Commander Shepard. Is anyone out there? ...Damnit!" Not so much luck. And here she was, unarmed and dubiously armored, standing in a ship that was _redefining_ the term "hostile territory", and she had no contact with anyone out there, or even any clue as to what was happening.

The only way to go was forward, so that was where she went. Still not at a hundred percent, she limped through from room to room, seeing increasingly startling images of people—asari, humans, batarians... _others_—behind glass-like surfaces or in the distance on other catwalks performing various repetitive tasks, most of which seemed to be pointless. The layout had an eerie glow and everything pulsed with a distinct and very wrong life. Or maybe that was just how the light settled on these disturbingly organic structures.

A gun was most likely out of the question, so she had to be careful. When she came to a long hallway of indoctrinated people, her only course of action was to duck down into a crawl space and hope that she didn't get lead into live wiring or a trash chute.

"_Protect… waiting for more informa… looks like Hell through here, bu…"_

A voice, distorted from the surrounding static, cut through on her comm as she moved. Her heart skipped a beat, though it was obvious from the chatter that communication was going to be difficult. Still, at least _someone_ was going on out there. Maybe when the signal improves, she'd be able to reconnect with brass and work out something from in here to their advantage. After all, she was as deep in as they can get.

As far as she could tell, maybe her progress was improving the comm. feed. She might've been in a part of the Reaper that blocked errant waves, and could be going towards an area more naked to the signal.

It was worth a shot, and if that wasn't incentive, nothing was. "Anyone on this signal, this is Commander Shepard."

Someone seemed to hear her, but it wasn't clearing up. She couldn't make out what the voice was saying. When it looked like she was coming towards an end to her cramped tunnel, she hurried as best she could and pulled herself out into another room. The lights were too low to determine anything, but there was no movement.

The static managed to clear up exponentially with her new location, and she repeated her inquiry.

"_Commander Shepard?"_ a familiar voice called, _"Damned if you weren't the last person I expected to hear. The extended comms are filled with chatter; I can't manage to get to anyone outside to help. You don't suppose I could give you my position so you could lend a hand?"_

"Is that you, Bailey? I'm not sure I can reach you from my location. I don't even know if we're in the same arm of the galaxy."

"_Well, this channel is a local one, so you can't be too far."_

"Local?" Shepard's thoughts were interrupted as she registered a flickering of light to her left. She clamped her mouth shut and turned, seeing that the nearby wall had some dull, yellow illumination from inside a pod-like structure. It hit to her something of familiarity, but she couldn't really place it.

Behind the glass, she could see a form within the low light. It was strange and hunched over, much of it's body covered with wires and tubes, but she could make out shoulders and a head.

And a face.

Eyes opened and sprang to center on hers, and the scream of some strange, bird-like animal ripped ripped from its opened mouth and was muffled by the structure surrounding it. Its alien hands rose and scrabbled at the glass around it, pounding and screaming something unknown to her translators. Forms within lights all around her woke up with the commotion, and each added more and more of their own howls and cries until the sound was deafening. She turned this way and that, in a defensive stance, her heart racing as she realized what this was.

Whatever these aliens were, they were to be harvested. Their purpose here was to be liquefied into genetic goo, just like the humans abducted from the colonies by the Collectors.

"My god… they're making another one! And hiding it in another Reaper?" She leapt forward and tried to pry off the lid of the first one she saw. The thing inside, whatever it was, saw her attempts and shouted in a low croon, clawing at the side she was working on. Whatever it was, whether or not it was dangerous, Shepard reasoned, it didn't deserve to be processed into a Reaper.

A pressure slammed down on her from all sides, along with the blare of a low voice. "SHEPARD."

She groaned and buckled under the pressure, but did not fall and managed to prop herself up against the yellowish glass. The creatures within the pods moaned in similar anguish. "Harbinger," she said back at it.

"YOU WILL NOT ESCAPE YOUR ASCENDANCE, SHEPARD."

"Of all the pregnant Reapers to be inside, it had to be you." Her feet steadied and she managed to pull herself up, then went towards what looked like an exit. "But I've still got shit to do if you're around, so I'm not about to stick around to chat."

"SHEPARD HAS BEEN LOCATED. CAPTURE ALIVE IF POSSIBLE."

Before she knew it, she was sprinting through hallway after hallway of groaning unknowns locked in processing pods. Walls shut in on her and forced her to change direction. Various beams and whatever rose up under her feet to trip or trap her, making her stumble and only able to keep balance for her momentum. Indoctrinated creatures of various races descended on her in flocks. Their hands grabbed and snatched at her incessantly. They chased her and the natural biotic of asari flew at her and threw her against walls, but she managed to pull herself up and move on.

"_Shepard! I think I'm able to track you down based on your signal! It's not easy but—holy shit!"_

"What can you give me here, Bailey?" A salarian popped up in front of her and she managed to grab him by the horns and slam him into a wall. "Because I could really use a little back-up right about now."

"_You didn't tell me you were right next to a goddamn Reaper!"_

"Next to? I've got some news for you… damnit!" Her trajectory led her to a dead end. She whipped around to look at the approaching indoctrinated hoard, trampling over each other like a living wall.

She didn't have time to make her peace, because an eruption of sound came with the flooding of light as the wall behind her tore away. A powerful, black-blue energy surrounded it and pulled it away like it was taffy, and the whine of metal being ripped echoed before it was flung into the brightness. Without a thought, she leapt blind into the opening.

The drop was several meters and the landing was hard, even with the roll. In a second, Bailey was at her side and pulling her to stand. "You alright there?"

"Working on it." She looked up to the make-shift door.

Of all people, it was Aria, Queen of Omega, floating above and eradicating the whole group of hostiles with her biotics for all she was worth. Shepard couldn't help but gawk in confusion.

With a final grunt, she pushed the remaining away and landed next to the two watching, smiling despite herself and what looked to be some very obvious wounds. Maybe she enjoyed getting her hands dirty from time to time. "You know, Shepard, people really don't know what they're talking about when they label you as 'unpredictable'. Go where shit's hit the worst and there you are, right in the middle of it."

Shepard found herself grinning as well. "Strange as it is to say, it's good to see the attacks on the Citadel haven't brought you down."

"Like _hell_ if I'm just going to roll over and die while Cerberus still has my rock."

* * *

That bit about the shaft of hands is referencing a scene from "Labyrinth".

This chapter requires a little more development than the usual level building, particularly in inventing new aliens. But the aliens in question aren't necessary to the plot or gameplay other than being different, so development could be as minor as taking pre-existing models and shapes and messing with them.


End file.
